Recent advances in the biological sciences require new approaches for high throughput analytical systems. One way to achieve high throughput is to use multiple capillary electrophoresis separation columns run in parallel. For example, over one hundred separation columns are currently used in capillary array DNA sequencers. Similar systems may be used for other applications, such as protein and peptide analysis and/or analysis of small molecules. Many other separation principles besides capillary electrophoresis, such as liquid chromatography, electrochromatography, extraction, etc., are also useful for analysis of molecular components of biological systems and are amenable to multiplexing in some form of an array. Such arrays may be composed, e.g., of individual columns (or groups of individual columns) or may be completely integrated, for example on a microfabricated device. To ensure stable physico-chemical conditions during a separation procedure, the array must be operated under a defined constant or programmed temperature or temperature gradient. In existing DNA sequencers or analyzers, for example, all of the separation columns are held at the same temperature.